Phlya

adjustText

A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.

hicplotlib

coolpuppy_paper

Code and data used to replicate the analysis in the coolpup.py paper

hmm_bigwigs

using hmm on bigwigs

Hi-CSGE

[DEPRECATED} A pipeline fastq->heatmaps for an SGE cluster based on hiclib

bioconda-recipes

Conda recipes for the bioconda channel.

biopython

Official git repository for Biopython (converted from CVS)

C-integration-mapping

[wip] mapping integration sites of defined sequences using Hi-C-like data

C-TALE-Normalization

Code and examples for C-TALE normalization

CoolBox

Jupyter notebook based genomic data visualization toolkit.

cooler

A cool place to store your Hi-C

cooltools

The tools for your .cool's

distill-reorder-C

snakemake workflow to analyze Hi-C-like data for multiple versions of the reference genome

higlass

Fast large scale matrix visualization for the web.

higlass-python

Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer

ImageScripts

Some scripts for image analysis

liftOverBedpe

A liftOver wrapper to accomodate BEDPE files

manual_Bonev

Finishing distiller processing of Bonev's data manually to avoid re-doing filtering

multiprocessing-logging-feedstock

A conda-smithy repository for multiprocessing-logging.

mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

peaktools

tools for BEDPE-style peaks

pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks

pysradb

Package for fetching metadata and downloading data from SRA/ENA

resgen-python

scikit-image

Image Processing SciKit (Toolbox for SciPy)

selfish

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.

snakemake-qsub

Simple snakemake profile for qsub cluster

snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

tagmap

Map insertions of transopable elements using tagmentation

viscm

A tool for visualizing and designing colormaps using colorspacious and matplotlib